/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_RF_DIAGONAL_ALG_H_
#define _U2_RF_DIAGONAL_ALG_H_

#include <QMutex>

#include "RFBase.h"

namespace U2 {

class RFDiagonalWKSubtask;

class RFDiagonalAlgorithmWK : public RFAlgorithmBase {
    Q_OBJECT
    friend class RFDiagonalWKSubtask;

public:
    RFDiagonalAlgorithmWK(RFResultsListener *rl, const char *seqX, int sizeX, const char *seqY, int sizeY, DNAAlphabetType seqType, int w, int k);

    void prepare();

protected:
    int START_DIAG;
    int END_DIAG;
};

class RFDiagonalWKSubtask : public Task {
    Q_OBJECT
    friend class RFDiagonalAlgorithmWK;

public:
    RFDiagonalWKSubtask(RFDiagonalAlgorithmWK *owner, int threadNum, int totalThreads);

    void run();

private:
    void processDiagonal(int x, int y);
    int getDiagLen(int d) const;
    int processMatch(const char *x, const char *y, const char *xEnd, const char *yEnd, int c);

    RFDiagonalAlgorithmWK *owner;

    int threadNum;
    int nThreads;
    const char *dataX;
    const char *dataY;

    QVector<RFResult> diagResults;

    quint64 areaS;
    quint64 currentS;
    quint64 nextPercentS;
};

}    // namespace U2

#endif
